Data from: Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect

How polymorphisms are maintained within populations over long periods of
time remains debated, because genetic drift and various forms of selection
are expected to reduce variation. Here, we study the genetic architecture
and maintenance of phenotypic morphs that confer crypsis in Timema
cristinae stick insects, combining phenotypic information and
genotyping-by-sequencing data from 1360 samples across 21 populations. We
find two highly divergent chromosomal variants that span megabases of
sequence and are associated with color polymorphism. We show that these
variants exhibit strongly reduced effective recombination, are
geographically widespread, and probably diverged millions of generations
ago. We detect heterokaryotype excess and signs of balancing selection
acting on these variants through the species’ history. A third chromosomal
variant in the same genomic region likely evolved more recently from one
of the two color variants and is associated with dorsal pattern
polymorphism. Our results suggest that large-scale genetic variation
associated with crypsis has been maintained for long periods of time by
potentially complex processes of balancing selection.